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ols_lookup.py
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ols_lookup.py
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# Licensed to the Technische Universität Darmstadt under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The Technische Universität Darmstadt
# licenses this file to you under the Apache License, Version 2.0 (the
# "License"); you may not use this file except in compliance
# with the License.
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
from fastapi import FastAPI, HTTPException
import uvicorn
import requests
from fastapi.params import Query
app = FastAPI()
def get_ols_item(iri):
url = f"https://www.ebi.ac.uk/ols/api/terms/{iri}"
response = requests.get(url)
response.raise_for_status()
data = response.json()
result = {
"id": iri,
"l": data.get('label', ''),
"d": data.get('description', '')
}
return result
def search_ols(query, limit=10):
url = 'https://www.ebi.ac.uk/ols/api/select'
params = {
'q': query,
'rows': limit,
}
response = requests.get(url, params=params)
response.raise_for_status()
data = response.json()
seen_iris = set()
unique_results = []
for item in data.get('response', {}).get('docs', []):
iri = item.get('iri', '')
if iri not in seen_iris: # Skip duplicate IRIs
seen_iris.add(iri)
description = item.get('description', [])
result = {
'id': iri,
'l': item.get('label', ''),
'd': description[0] if description else '',
}
unique_results.append(result)
return unique_results
@app.get("/")
async def lookup(item_id: str = Query(None, alias="id"), query: str = Query(None, alias="q"),
limit: int = Query(None, alias="l"),
query_context: str = Query(None, alias="qc")):
if item_id:
return get_ols_item(item_id)
if query:
return search_ols(query, limit)
return []
if __name__ == "__main__":
uvicorn.run(app, host="0.0.0.0", port=8888)